4OL8: Ty3 reverse transcriptase

Ty3 reverse transcriptase bound to DNA/RNA. Determined by X-ray diffraction at 3.1 Å resolution. Released 5 Mar 2014.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 14,105
Mol. weight: 241.73 kDa
Released: 5 Mar 2014

Explore 4OL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OL8 contains 99 α-helices and 112 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	23-28	6
β-strand	51	1	1
α-helix	54	1
β-strand	55	1	2
α-helix	56	1
β-strand	63	1	3
α-helix	64-68	5
α-helix	73-86	14
β-strand	90-91	2	4
β-strand	98	1	3
β-strand	99	1	5
β-strand	101-105	5	6
β-strand	111-115	5	6
α-helix	118-121	4
β-strand	124	1	2
α-helix	134-138	5
β-strand	146-151	6	7
β-strand	152	1	8
α-helix	155-158	4
β-strand	160	1	9
β-strand	161	1	1
α-helix	162	1
α-helix	163-169	7
β-strand	171-172	2	5
β-strand	177-178	2	5
β-strand	179-180	2	4
β-strand	182	1	9
α-helix	190-202	13
β-strand	208-211	4	7
β-strand	214-219	6	7
α-helix	222-238	17
β-strand	243	1	8
α-helix	245-247	3
β-strand	257	1	10
β-strand	260-262	3	10
β-strand	267-269	3	10
α-helix	271-274	4
α-helix	286-297	12
α-helix	306-309	4
α-helix	328-336	9
β-strand	352-356	5	11
β-strand	364-371	8	11
β-strand	379-386	8	11
α-helix	397-409	13
α-helix	413-416	4
β-strand	422-424	3	11
α-helix	441-451	11
β-strand	457-458	2	11

Chain B: 29 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	23-28	6
α-helix	37-40	4
β-strand	51	1	12
α-helix	54	1
β-strand	55	1	13
α-helix	56	1
α-helix	59-62	4
β-strand	63	1	14
α-helix	64-68	5
α-helix	71-87	17
β-strand	90-92	3	15
β-strand	98	1	14
β-strand	99	1	15
β-strand	101-104	4	16
β-strand	112-115	4	16
α-helix	118-123	6
β-strand	124	1	13
α-helix	128-130	3
α-helix	134-141	8
β-strand	146-150	5	17
α-helix	153-155	3
β-strand	160	1	18
β-strand	161	1	12
α-helix	162	1
α-helix	163-169	7
β-strand	171-173	3	15
β-strand	176-180	5	15
β-strand	182	1	18
α-helix	190-202	13
β-strand	208-210	3	17
β-strand	215-219	5	17
α-helix	222-238	17
α-helix	245-247	3
β-strand	249-252	4	17
β-strand	255-257	3	19
β-strand	260-262	3	19
β-strand	267-269	3	19
α-helix	275-278	4
α-helix	281-283	3
α-helix	286-298	13
α-helix	300-302	3
α-helix	311-318	8
α-helix	325-338	14
β-strand	344	1	20
β-strand	352-359	8	20
β-strand	363-371	9	20
β-strand	377-387	11	20
α-helix	397-411	15
α-helix	413-416	4
β-strand	420-425	6	20
α-helix	430-434	5
α-helix	438-440	3
α-helix	441-444	4
α-helix	447-450	4
β-strand	454-459	6	20
α-helix	466-473	8

Chain E: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	24-28	5
β-strand	51	1	31
β-strand	55	1	32
β-strand	63	1	33
α-helix	64-66	3
α-helix	71-84	14
β-strand	90-91	2	34
β-strand	98	1	33
β-strand	99-100	2	35
α-helix	118-121	4
β-strand	124	1	32
α-helix	134-137	4
β-strand	146-149	4	36
β-strand	150-151	2	37
β-strand	152	1	38
α-helix	155-158	4
β-strand	160	1	39
β-strand	161	1	31
α-helix	162	1
α-helix	163-165	3
α-helix	167-169	3
β-strand	171-172	2	35
β-strand	177-178	2	35
β-strand	179-180	2	34
β-strand	182	1	39
α-helix	190-202	13
β-strand	208-211	4	37
β-strand	214-217	4	37
β-strand	218-219	2	36
α-helix	222-238	17
β-strand	243	1	38
β-strand	249-252	4	36
β-strand	255-257	3	40
β-strand	260-262	3	40
α-helix	273-279	7
α-helix	281-282	2
α-helix	287-290	4
α-helix	293-297	5
α-helix	307-310	4
β-strand	355-356	2	41
β-strand	363-367	5	42
β-strand	383-387	5	42
α-helix	399-404	6
α-helix	407-411	5
α-helix	413-416	4
α-helix	421	1
β-strand	422-424	3	41
α-helix	441-450	10
β-strand	456-457	2	41

Chain F: 29 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	23-28	6
β-strand	33-34	2	21
α-helix	37-41	5
β-strand	51	1	22
α-helix	54	1
β-strand	55	1	23
α-helix	56	1
α-helix	59-62	4
β-strand	63	1	24
α-helix	64-68	5
α-helix	71-86	16
β-strand	90-92	3	25
β-strand	98	1	24
β-strand	99-100	2	25
β-strand	101-105	5	26
β-strand	111-115	5	26
α-helix	118-122	5
β-strand	124	1	23
α-helix	125-126	2
α-helix	128-130	3
α-helix	137-141	5
β-strand	146-150	5	27
α-helix	153-155	3
β-strand	160	1	28
β-strand	161	1	22
α-helix	162	1
α-helix	163-169	7
β-strand	171-173	3	25
β-strand	176-180	5	25
β-strand	182	1	28
α-helix	190-202	13
β-strand	208	1	27
β-strand	215-219	5	27
α-helix	222-238	17
α-helix	241-242	2
β-strand	243-244	2	21
α-helix	245-247	3
β-strand	249-252	4	27
β-strand	255-257	3	29
β-strand	260-263	4	29
β-strand	266-269	4	29
α-helix	275-278	4
α-helix	290-296	7
α-helix	299-302	4
α-helix	306-309	4
α-helix	331-337	7
β-strand	344	1	30
β-strand	353-360	8	30
β-strand	363-371	9	30
β-strand	377-386	10	30
α-helix	398-411	14
α-helix	413-416	4
β-strand	421-425	5	30
α-helix	430-434	5
α-helix	439-440	2
α-helix	447-450	4
β-strand	455-459	5	30
α-helix	468-472	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Reverse transcriptase/ribonuclease H	A, B, E, F	protein	478	Saccharomyces cerevisiae	Q99315 (AlphaFold model)
5'-r(cpupgpapgpapgpapgpapgpgpapapgpapupg)-3'	C, G	RNA	18
5'-d(cpaptpcptptpcpcptpcptpcptpcptpc)-3'	D, H	DNA	16

Sequence of entity 1 (A, B, E, F), FASTA

>4OL8_1 Reverse transcriptase/ribonuclease H (chains A, B, E, F)
GPTIQSVEPNATDHSNKDTFCTLPVWLQQKYREIIRNDLPPRPADINNIPVKHDIEIKPG
ARLPRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDGTFRLCVDYR
TLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAFVTPSGKY
EYTVMPFGLVNAPSTFARYMADTFRDLRFVNVYLDDILIFSESPEEHWKHLDTVLERLKN
ENLIVKKKKCKFASEETEFLGYSIGIQKIAPLQHKCAAIRDFPTPKTVKQAQRFLGMINY
YRRFIPNCSKIAQPIQLFICDKSQWTEKQDKAIDKLKDALCNSPVLVPFNNKANYRLTTD
ASKDGIGAVLEEVDNKNKLVGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHG
KHFTLRTNHISLLSLQNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISRAVY

Sequence of entity 2 (C, G), FASTA

>4OL8_2 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3' (chains C, G)
CUGAGAGAGAGGAAGAUG

Sequence of entity 3 (D, H), FASTA

>4OL8_3 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3' (chains D, H)
CATCTTCCTCTCTCTC

Primary citation

Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry. Nowak, E., Miller, J.T., Bona, M.K. et al. Nat Struct Mol Biol (2014) 21:389-396. DOI 10.1038/nsmb.2785 · PubMed

Other PDB entries of the same protein (UniProt Q99315 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q5B 3.98 Å, Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene

Browse structure collections

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